Many enterprises are interested in using the IS development methodologies as a means of increasing system performance and solving the problems of delayed delivery time, excessive budget, and failure of integrated systems. Even if previous researches showed that the system productivity and quality improvement using the system development methodologies are very poor, we tried to find that the methodologies are meaningful as an innovative means for IS performance. We defined that the IS development methodology as a technical and managerial innovation for IS department. We intended to study the relationship between the implementation process of the IS development methodology divided into four steps and IS performance. A cross-sectional field survey with IS departments of domestic companies was conducted, and we used LISREL 8.12a to perform the structural equation model analysis and hypothesis verification. We found the meaningful relationship between the development methodology and qualitative performance. We reconfirmed that the relationship between the development methodology and quantitative performance is not meaningful as expected, which is the same result with the previous researches. But the qualitative performance affects very strongly to the quantitative performance. As a results, we suggest that IS managers and developers keep the principles of the IS development methodologies to get the quantitative performance through the qualitative performance improvement.